ROI Pairs (Anchor-Target) Analysis
TROVE (KAG)
1/20/20
- 1. Basic setup
- 2. Read image list file
- 3. Get ROI pairs set for a given HEMI, ANCHOR_REGION combo
- 4. Do basic sanity checking on the time series
- 5. Compute the correlations
- 6. Do basic sanity checking on the correlations
- 7. Do the sample ANOVA with FDR
- 8. Post process the sample ANOVA (significant ROI pairs) with post hoc t-tests
- 9. Do the permutation ANOVA with multiple hypothesis correction
- 10. Determine the significant post hoc t tests based on permutation ANOVA FDR p value
- 11. Post process the sample ANOVA (significant ROI pairs) post hoc t-tests with adjusted FDR corrected p value
- 12. Generate file lists for AFNI images
- 13. Generate spaghetti plots
- 14. Generate cluster analysis
- 15. Deep-dive post hoc t-test results
ADNI3 - ROI Pairs Analysis
- Basic setup, file directories, file names
- Read image list file
- Get ROI pairs set for a given HEMI, ANCHOR_REGION combo
- Do basic sanity checking on the time series
- Compute the correlations
- Do basic sanity checking on the correlations
- Do the sample ANOVA with FDR
- Post process the sample ANOVA (significant ROI pairs) post hoc t-tests
- Do the permutation ANOVA
- Update the ANOVA sampe FDR corrected p value with ANOVA permutation results
- Post process the sample ANOVA (significant ROI pairs) post hoc t-tests with adjusted FDR corrected p value
- Generate tables and graphs for publication
1. Basic setup
2. Read image list file
## rid id_mri id_fmri dx dxbl
## 1 002_S_0413 I863056 I863058 CN CN
## 2 002_S_1261 I989320 I989324 MCI CN
## 3 002_S_4473 I827361 I827363 MCI EMCI
## 4 002_S_4654 I848000 I848004 MCI LMCI
## 5 002_S_6007 I988538 I988542 CN SMC
## 6 002_S_6030 I861965 I861967 CN SMC
## 7 002_S_6103 I938767 I938771 CN SMC
## 8 003_S_1122 I1020423 I1020436 MCI LMCI
## 9 003_S_6067 I912447 I912451 CN CN
## 10 003_S_6258 I973293 I973297 MCI EMCI
## 11 003_S_6268 I1005884 I1005896 MCI EMCI
## 12 006_S_4357 I964841 I964844 CN CN
## 13 006_S_4960 I1003607 I1003610 CN LMCI
## 14 006_S_6252 I969773 I969776 MCI LMCI
## 15 006_S_6291 I989656 I989659 MCI LMCI
## 16 006_S_6441 I1020186 I1020189 MCI LMCI
## 17 011_S_0021 I957745 I957749 CN CN
## 18 011_S_4105 I915862 I915866 CN CN
## 19 011_S_6418 I1009810 I1009814 CN CN
## 20 012_S_5157 I1116800 I1116805 CN SMC
## 21 012_S_5195 I1071932 I1072832 CN SMC
## 22 014_S_6148 I951357 I951360 CN SMC
## 23 014_S_6424 I1037394 I1037397 CN SMC
## 24 014_S_6522 I1037958 I1037960 CN SMC
## 25 018_S_2155 I905773 I905776 MCI EMCI
## 26 018_S_2180 I1051277 I1051285 MCI EMCI
## 27 018_S_4400 I909607 I909610 CN CN
## 28 018_S_6351 I995861 I995864 CN CN
## 29 019_S_6315 I990219 I990223 MCI LMCI
## 30 019_S_6483 I1020137 I1020140 MCI LMCI
## 31 020_S_5140 I935824 I935828 CN SMC
## 32 020_S_5203 I1086072 I1086079 CN SMC
## 33 020_S_6185 I958011 I958015 CN CN
## 34 022_S_5004 I973603 I973606 MCI EMCI
## 35 022_S_6069 I895057 I895059 CN SMC
## 36 024_S_5290 I904007 I904009 CN SMC
## 37 031_S_4021 I1086094 I1086097 CN CN
## 38 032_S_4277 I1025881 I1025885 CN CN
## 39 032_S_5289 I996840 I996828 CN SMC
## 40 032_S_6279 I981036 I981034 CN SMC
## 41 032_S_6293 I993285 I993281 CN CN
## 42 035_S_6200 I964917 I964919 CN SMC
## 43 035_S_6488 I1019265 I1019267 CN CN
## 44 037_S_4028 I927511 I927515 CN CN
## 45 037_S_4410 I824980 I824984 CN CN
## 46 037_S_6144 I944650 I944654 CN CN
## 47 041_S_1418 I882537 I882539 MCI LMCI
## 48 041_S_4427 I915902 I915906 CN CN
## 49 041_S_4876 I872923 I872925 MCI EMCI
## 50 041_S_5100 I881729 I881731 CN SMC
## 51 041_S_6136 I944422 I944424 CN CN
## 52 041_S_6401 I1008726 I1008728 CN SMC
## 53 053_S_5296 I1079463 I1079466 CN SMC
## 54 068_S_0802 I878974 I878976 MCI LMCI
## 55 068_S_4424 I892735 I892737 CN CN
## 56 068_S_4431 I913456 I913458 MCI EMCI
## 57 082_S_2121 I963756 I963758 MCI EMCI
## 58 082_S_4428 I947589 I947591 CN CN
## 59 082_S_5278 I969187 I969190 CN SMC
## 60 082_S_6197 I992246 I992249 CN SMC
## 61 082_S_6283 I992286 I992291 CN CN
## 62 082_S_6563 I1051051 I1051055 CN SMC
## 63 094_S_2201 I916812 I916814 CN EMCI
## 64 094_S_6250 I979816 I979818 CN SMC
## 65 100_S_4556 I928482 I928485 CN EMCI
## 66 114_S_6309 I992776 I992775 CN SMC
## 67 116_S_4453 I958094 I958096 CN CN
## 68 116_S_6119 I957994 I957997 CN SMC
## 69 116_S_6428 I1017005 I1017007 MCI LMCI
## 70 116_S_6439 I1015823 I1015826 CN CN
## 71 123_S_0072 I922176 I922179 CN CN
## 72 123_S_6118 I927419 I927422 CN SMC
## 73 130_S_4817 I841950 I841953 MCI LMCI
## 74 130_S_6019 I854993 I854996 CN SMC
## 75 130_S_6037 I873168 I873171 CN SMC
## 76 130_S_6319 I990195 I990198 CN SMC
## 77 130_S_6372 I1001329 I1001332 CN SMC
## 78 141_S_6041 I871844 I871842 MCI EMCI
## 79 141_S_6061 I1116406 I1116411 MCI SMC
## 80 141_S_6253 I974714 I974704 CN SMC
## 81 141_S_6423 I1018387 I1018395 CN CN
## 82 168_S_6062 I892771 I892773 CN SMC
## 83 168_S_6085 I916399 I916401 CN CN
## 84 177_S_6335 I995457 I995459 CN SMC
## 85 177_S_6409 I1029048 I1012536 CN SMC
## 86 301_S_6224 I963152 I963156 CN CN
## 87 305_S_6157 I958026 I958031 CN CN
## 88 305_S_6188 I968581 I968584 CN CN
## 89 305_S_6498 I1019281 I1019284 MCI EMCI
## 90 941_S_4292 I893552 I893554 CN CN
## 91 941_S_6017 I852748 I852750 MCI LMCI
## 92 941_S_6054 I880643 I880645 CN CN
## 93 941_S_6058 I884964 I884966 CN SMC
## 94 941_S_6068 I893045 I893047 MCI LMCI
## 95 941_S_6094 I921879 I921881 CN CN## # A tibble: 4 x 2
## dxbl n
## <chr> <int>
## 1 CN 33
## 2 EMCI 13
## 3 LMCI 14
## 4 SMC 35## # A tibble: 2 x 2
## dx n
## <chr> <int>
## 1 CN 69
## 2 MCI 263. Get ROI pairs set for a given HEMI, ANCHOR_REGION combo
4. Do basic sanity checking on the time series
## [1] 0
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.0002909 0.0003985 0.0004432 0.0004499 0.0005039 0.0006323## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.1338 0.3174 0.4436 0.5801 0.7086 6.9380
## [1] 0
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.0002890 0.0003987 0.0004438 0.0004499 0.0005038 0.0006342## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.07961 0.26009 0.34326 0.44323 0.49408 6.28562
5. Compute the correlations
6. Do basic sanity checking on the correlations
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## -0.08065 0.03912 0.07074 0.07922 0.10698 0.75683## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.0734 0.1200 0.1324 0.1348 0.1464 0.2494
7. Do the sample ANOVA with FDR
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.0000003 0.0005872 0.0020894 0.0070387 0.0065790 0.4068631
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.9778 4.3452 5.2880 5.4546 6.3504 13.4201
8. Post process the sample ANOVA (significant ROI pairs) with post hoc t-tests
## p
## Min. :2.510e-07
## 1st Qu.:3.935e-04
## Median :1.272e-03
## Mean :2.009e-03
## 3rd Qu.:3.035e-03
## Max. :7.818e-03
9. Do the permutation ANOVA with multiple hypothesis correction
10. Determine the significant post hoc t tests based on permutation ANOVA FDR p value
## Post-process Permutation ANOVA FDR ( q= 0.005 ) p Value = 0.00311. Post process the sample ANOVA (significant ROI pairs) post hoc t-tests with adjusted FDR corrected p value
## Sample-based post hoc t-test FDR-corrected p values:## Permutation-based post hoc t-test FDR-corrected p values:## smc_cn_t_pstar emci_cn_t_pstar lmci_cn_t_pstar emci_smc_t_pstar
## 1 0.0005365496 0.0005992598 0.0007027061 0.0004896183
## lmci_smc_t_pstar lmci_emci_t_pstar
## 1 0.000180546 0.0012889812. Generate file lists for AFNI images
13. Generate spaghetti plots
14. Generate cluster analysis
## mean_by_dx
## 1 2 3 4 5 6 7
## 349 195 12 264 566 311 763
15. Deep-dive post hoc t-test results
## smc_cn emci_cn lmci_cn emci_smc lmci_smc lmci_emci
## 1 264 295 347 241 89 636
